Persistent and chronic infections are maintained by a dynamic modulation of microbe - host cell interactions. During this process, microorganisms evolve and adapt to the host by regulating the expression of different genes, in particular those involved in virulence. At the bacterial population level, specific (possibly hypervirulent) clones may predominate at different times in individuals as well as groups of patients. The timely storage of microbial pathogens in the microbiology laboratory together with the availability of clinical data from the patients allows following the virulence traits, host adaptation and changing epidemiology of the pathogens. Three specific examples are summarized below: 1) We have performed extensive molecular identification and typing of 42 clinical isolates of M. abscessus and the closely related newly-described species M. massiliense and M bolletii from patients followed at the NIH between 1999 and 2007. This work lead to the identification of characteristic clonal groups for each species, including two major clonal clusters for M. abscessus and one for M. massiliense. In particular, we identified a distinct group of strains with mixed features of M. abscessus and M. massiliense. Pan-mycobacterial microarray platforms are being currently used to reveal genomic differences among these clonal groups. 2) We studied six strains of Burkholderia multivorans from chronic granulomatous disease (CGD) patients, cystic fibrosis patients and the environment. Cell association (bound and/or ingested bacteria) and invasion (ingested bacteria), and cytokine induction in peripheral blood monocytic cells (PBMCs), monocytes, and neutrophils from normal donors and CGD patients were examined. One clinical strain showed the highest cellular association (68.6% of normal monocytes), whereas for the environmental isolate it was only 7.9%. All strains of B. multivorans associated significantly more to CGD PBMCs and neutrophils than to normal control cells. Two strains from CGD patients were highly virulent in a mouse model of CGD, while the environmental isolate was avirulent. Whole genome sequencing of the clinical strains has been recently completed leading to the initiation of comparative genomics aimed to the identification of virulence factors. 3) Over an 8-month period, five sequential isolates of B. petrii were grown from a female patient with pulmonary nodular bronchiectasis and nontuberculous mycobacterial infection. Molecular typing demonstrated that although related, the successive clinical isolates had distinct genetic differences, and all five were different from the two reference strains (the environmental type strain and the first described clinical strain). Immunoblots showed a strong immune response by the patient against her isolates 1, 2, 4 and 5 but not her isolate 3 or the two reference strains. Gel analysis of purified LPS from isolate 1 showed bands for LPS inner core, outer core and O-antigen. Interestingly, the O-antigen band was also present in the LPS of the environmental type strain but was missing in the LPS of isolate 3 and the reference clinical strain. The changes in the LPS of B. petrii exemplify the creative strategies used by pathogens for host persistence. Whole genome sequencing of isolates 1, 3, 4 and 5 has been recently completed and is aimed to provide light on mechanisms of modulation of bacterial virulence and adaptation to the host during chronic infection. We believe lessons learned from B. petrii can be applied to other Bordetella spp such as B. pertussis, which is still highly prevalent despite extensive vaccination programs.